Cat. No. EM07.1 Version: 1.2017 NEW VERSION Kit for DNA purification after enzymatic reactions EXTRACTME is a registered trademark of BLIRT S.A.
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Cat. No. EM07.1 I. INTENDED USE The EXTRACTME DNA CLEAN-UP KIT is designed for a rapid and efficient purification of DNA fragments after enzymatic reactions. It efficiently removes nucleases, primers, enzyme inhibitors, detergents, restriction enzymes, polymerases, divalent ions, salts, and mineral oil, etc. Purified DNA may be used in common downstream alications. Primers from PCR reactions are eliminated quantitatively while small DNA fragments are still bound and purified with high recovery. The kit enables purification of DNA fragments from 50 bp to 20 kb, as well as plasmid and genomic DNA. The purification protocol and buffer formulations were optimized for high yields and purity of DNA. The product is intended for research use only. II. COMPONENTS OF THE KIT AND STORAGE CONDITIONS NUMBER OF 10 50 250 Catalogue number EM07.1-010 EM07.1-050 EM07.1-250 CB Buffer (Binding Buffer) 4 ml 20 ml 100 ml CW Buffer (conc.) * (Wash Buffer) 3.5 ml 16 ml 80 ml Elution Buffer 2 ml 10 ml 5 x 10 ml DNA Purification Columns 10 pcs 50 pcs 5 x 50 pcs Collection Tubes (2 ml) 10 pcs 50 pcs 5 x 50 pcs Loading Buffer 1 pc 1 pc 1 pc * Prior to the first use, add an aropriate amount of 96-100% ethanol to the CW Buffer (see the instructions on the bottle label and in the table below). It is recommended to mark the bottle containing added alcohol. NUMBER OF 10 50 250 Catalogue number EM07.1-010 EM07.1-050 EM07.1-250 CW Buffer 3.5 ml 16 ml 80 ml 96-100% ethanol 14 ml 64 ml 320 ml Total volume 17.5 ml 80 ml 400 ml All kit's components should be stored at room temperature (15-20 C). In order to avoid evaporation, ensure that all buffer bottles are tightly closed before storing. Under proper conditions the product can be stored until the expiry date (the information on the label) or at least for 12 months after first opening. 3
III. ADDITIONAL MATERIALS AND EQUIPMENT REQUIRED 96-100% ethanol PFA 1.5-2 ml sterile microcentrifuge tubes automatic pipettes and pipette tips personal protecion equipment (lab coat and gloves) microcentrifuge with rotor for 1.5-2 ml ( 11k x g) vortex mixer IV. PRINCIPLE DNA purification procedure utilizes spin minicolumns with membranes which efficiently and selectively bind nucleic acids. First, CB Buffer is added to DNA sample. It causes proteins to degrade and enables DNA to bind with the column's membrane. The binding buffer contains a color indicator, that facilitates an easy monitoring of the solution s ph for optimal DNA binding. The two-step washing stage efficiently removes impurities and enzyme inhibitors. Purified DNA is eluted using either a low ionic strength buffer (Elution Buffer) or water (ph 7.0-9.0) and may be used directly in all downstream alications such as PCR, qpcr, DNA sequencing, enzymatic restriction, and ligation, etc. or stored until ready to use. V. QUALITY CONTROL The quality of each production batch (LOT) of the EXTRACTME DNA CLEAN-UP Kit is tested with the use of standard QC procedures. Purified DNA concentration and quality are evaluated by gel electrophoresis and spectrophotometer. www.blirt.eu 4
Cat. No. EM07.1 VI. PRODUCT SPECIFICATIONS SAMPLE MATERIAL up to 200 μl of DNA sample YIELD ~60 to ~90%, depending on DNA fragment length DNA FRAGMENT LENGTH 50 bp ~20 kbp genomic and plasmid DNA, however the efficiency will be decreased BINDING CAPACITY arox. 25 μg DNA TIME REQUIRED 10 min for 6 PCR purifications VII. SAFETY PRECAUTIONS Use of sterile filter tips is recommended. Avoid cross-contamination of DNA between minicolumns. Guanidine salts residues may form highly reactive compounds when combined with oxidation compounds. In case of spillage, clean the surface with a detergent water solution. 5
VIII. RECOMMENDATIONS AND IMPORTANT NOTES DNA elution The optimal volume of the elution buffer used should be chosen in accordance with the amount of DNA in a sample and to the final DNA concentration expected. The use of 15-30 μl of the Elution Buffer is recommended. It is essential to aly the elution buffer precisely onto the centre of the membrane. In order to maximize DNA recovery, the following modifications should alied: Heat the elution buffer up to 70 C, aly onto the column and incubate at room temperature for 5 min. Carry out 2 or 3 elution steps with 15-30 μl of the elution buffer. To assure complete DNA salvage from membrane, use 200 μl of the elution buffer. Elution Buffer The Elution Buffer does not contain EDTA, which may interfere with some enzymatic reactions. ph monitoring The CB Buffer contains an indicator, which enables ph monitoring. Yellow indicates that the solution's ph is lower than 7.0 and guarantees an optimal DNA binding with the membrane. When the ph is higher than 7.0, solution turns pink. It usually haens when the ph of DNA sample considerably differs from the standard parameters of DNA treatment operations (ph>9.0). In this case, it is essential to add 10 μl of 3 M sodium acetate (ph 5.2). It will lower the ph, enabling the solution to bind efficiently with the minicolumn membrane. Loading Buffer Loading Buffer is provided for analysis of purified DNA samples with the use of electrophoresis. Loading buffer contains 3 dyes (bromophenol blue, xylene cyanol and orange G). The buffer is concentrated by a factor of six, thus, in order to obtain the most satisfying results mix 2 μl of the loading buffer with 10 μl of purified DNA. www.blirt.eu 6
Cat. No. EM07.1 IX. SAMPLE PREPARATION Transfer an aropriate amount of DNA sample (no more than 200 μl) to a sterile, 1.5-2 ml Eendorf tube. Prior to the purification process, DNA samples may be stored at +4 C under DNase-free conditions for a short time or frozen (-80 C is strongly recommended) for a longer period. Avoid repeated freeze/thaw cycles of DNA samples. X. PRIOR TO ISOLATION 1. Mix well each buffer sulied with the kit. 2. Ensure that ethanol has been added to the CW Buffer. If not, add aropriate amount of 96-100% ethanol (volumes can be found on bottles' labels or in the table given in the section II). 3. E x a m i n e t h e b u ff e r s. I f a s e d i m e n t o c c u r r e d i n a n y o f t h e m, i n c u b a t e a bottle containing the solution at 37 C, mix occasionally until the sediment has dissolved. Cool to the room temperature. 7
XI. ISOLATION PROTOCOL STEP 1 Add 2 volumes of the CB Buffer to a 1 volume of DNA sample (for example add 100 μl CB Buffer to a 50 μl PCR reaction) and vortex for 3 s. c cfor sample preparation method, see instructions given in section IX. Sample preparation. STEP 2 11 000 x g 30 s Centrifuge a tube briefly in order to recover any remaining liquid from the lid and transfer the whole volume of the mixture into DNA purification minicolumn placed in a collection tube. Centrifuge for 30 s at 11 000 x g. Discard the filtrate. Transfer the purification minicolumn to a new collection tube (2 ml). STEP 3 Add 700 μl CW Buffer and centrifuge for 30 s at 11 000 x g. 11 000 x g Discard the filtrate and reuse the collection tube. 30 s www.blirt.eu 8
Cat. No. EM07.1 Recommended: repeat previous washing step. Add 700 μl CW Buffer and centrifuge for 30 s at 11 000 x g. Discard the flow-through and reuse the collection tube. 11 000 x g 30 s STEP 4 Centrifuge for 1 min at 11 000 x g. Discard the collection tube and the flow-through. c cthe wash buffer contains alcohol, which may interfere with some enzymatic reactions and also decrease the elution efficiency. It is therefore vital to remove the alcohol completely from the minicolumn before elution. 11 000 x g 60 s STEP 5 Carefully transfer the purification minicolumn to a sterile 1.5 ml Eendorf microcentrifuge tube. Add 15-30 μl of the Elution Buffer, directly onto the purification minicolumn membrane. Incubate the minicolumn at room temperature for 1 min. Centrifuge for 1 min at 11 000 x g. Remove the minicolumn. Isolated DNA is ready for use in downstream alications or for short-term storage at +4 C or for long-term storage at -20 C. 11 000 x g 60 s 9
XI. TROUBLESHOOTING Problem Possible cause Solution Low yield of purified DNA. DNA flows out of the lanes in the agarose gel. Blurred bands in the gel electrophoresis image. Inhibition of downstream enzymatic reactions. Ineffective DNA binding with the membrane. Incomplete DNA elution from the membrane. The ph of the water used for elution is lower than 7.0. Ethanol was not added to the wash buffer. Purified DNA contains residual alcohol. The elution solution contains DNases. Purified DNA contains residual salts. Purified DNA contains residual alcohol. Ensure the mixture is yellow after adding the CB Buffer. If the colour turns pink, add 10 μl of 3 M sodium acetate, ph 5.2. Before alying the Elution Buffer to the membrane, heat it to 70 C. Aly the Elution Buffer directly to the centre of the membrane. Extend the incubation time with the Elution Buffer to 5 min. Perform a second elution. Use the Elution Buffer for DNA elution. Ensure that 96-100% ethanol was added to the CW Buffer before use. Repeat the isolation, ensuring that no residual CW Buffer is left in the purification column after centrifugation in step 4. Use a fresh elution solution. If water is used instead of the Elution Buffer, ensure that it is DNase-free. Perform all centrifugation steps at room temperature. Ensure that there is no sediment in the CW Buffer prior to use. Repeat the isolation, ensuring that no residual CW Buffer is left in the purification column after centrifugation in step 4. www.blirt.eu 10
Cat. No. EM07.1 XII. SAFETY INFORMATION CB Buffer Hazard H225, H302, H315, H319, H332, H336 P305+P351+P338, P302+P352, P210, P233 H302 Harmful if swallowed H332 Harmful if inhaled H315 Causes skin irritation H319 Causes serious eye irritation H336 May cause drowsiness or dizziness H225 Highly flammable liquid and vapour P264 Wash hands thoroughly after handling P270 Do not eat, drink or smoke when using this product P261 Avoid breathing dust/fumes/gas/mist/vapours/spray P271 Use only outdoors or in a well-ventilated area P280 Wear protective gloves/protective clothing/eye protection/face protection P210 Keep away from heat/sparks/open flames/hot surfaces. No smoking P233 Keep container tightly closed P240 Ground/bond container and receiving equipment P241 Use explosion-proof electrical/ventilating/lighting/equipment P242 Use only non-sparking tools P243 Take precautionary measures against static discharge P301+312 IF SWALLOWED: Call a POISON CENTER/doctor/if you feel unwell P330 Rinse mouth P304+340 IF INHALED: Remove person to fresh air and keep comfortable for breathing P302+352 IF ON SKIN: Wash with plenty of water P332+313 If skin irritation occurs: Get medical advice/attention P362 Take off contaminated clothing P305+P351+P338 P313 IF IN EYES: Rinse cautiously with water for several minutes. Remove contact lenses, if present and easy to do. Continue rinsing. Get medical advice/attention P370+378 In case of fire: Use water spray, CO 2, foam, powder; fight larger fires with spray or alcohol resistant foam to extinguish P403+233 Store in a well ventilated place. Keep container tightly closed P405 Store locked up P403+235 Store in a well ventilated place. Keep cool. 11
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